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Fitzroy Basin Resource Operation Plan Ecological Monitoring and Assessment Program, Background Information and Design

Report No. 02/21

Prepared by Richard Pearson, Garry Werren, Brad Pusey Australian Centre for Tropical Freshwater Research James Cook University, Qld 4811 Phone: 07-47814262 Fax: 07-47815589 Email: actfr@jcu.edu.au

Fitzroy Basin Resource Operation Plan Ecological Monitoring and Assessment Program ACTFR Report No. 02/21

TABLE OF CONTENTS
FITZROY BASIN RESOURCE OPERATION PLAN ECOLOGICAL MONITORING AND ASSESSMENT PROGRAM. PART 1 RESEARCH PROJECT BACKGROUND INFORMATION AND DESIGN ..........................................................................................................1 Introduction. .......................................................................................................................................1 Proposed research design. .................................................................................................................1 Statistical methods..............................................................................................................................4 Ecological Goals and Hypotheses (Table 3 etc.) ..............................................................................4 1. Water quality. .............................................................................................................................5 2. FPWF will stimulate recruitment, dispersal and spawning activity. ..........................................5 3. Flows will maintain river character and behaviour. ..................................................................5 4. Maintain waterhole habitats. ......................................................................................................5 6. Maintain riparian habitats ...........................................................................................................6 7. High flows will provide natural connectivity between watercourses and associated floodplain and wetland habitats to support natural flora and fauna. ...............................................................6 8. Mean wet season flow volume will maintain a) estuarine productivity, and b) estuarine habitats.............................................................................................................................................7 9. Maintain R&T species..................................................................................................................7 Selection of indicators, methods of data collection, time frames. ..................................................7 Indicator selection............................................................................................................................7 Timing and frequency of sampling. ..................................................................................................7 Benthic metabolism. .........................................................................................................................8 Macroinvertebrate community structure..........................................................................................8 Fish cohorts, community structure and fish movement. ...................................................................8 Turtles. ...........................................................................................................................................10 Physical and chemical characteristics of in-stream habitats.........................................................10 Riparian habitat, vegetation community structure and canopy cover. ..........................................11 Frogs. .............................................................................................................................................12 Bird community structure...............................................................................................................12 Estuarine indicators. ......................................................................................................................13 Mangrove community structure. ....................................................................................................13 Physical characteristics and estuarine geomorphology. ...............................................................13 Projected Costings............................................................................................................................13 General observations/impressions. .................................................................................................13 Style etc. ............................................................................................................................................13 FITZROY BASIN RESOURCE OPERATION PLAN ECOLOGICAL MONITORING AND ASSESSMENT PROGRAM. PART 1 RESEARCH PROJECT BACKGROUND INFORMATION AND DESIGN ........................................................................................................14 Preamble to 2nd draft, September 1, 2002 ......................................................................................15 Introduction. .....................................................................................................................................15 Proposed research design. ...............................................................................................................16 Statistical methods............................................................................................................................18 Ecological Goals and Hypotheses (Table 3 etc.) ............................................................................19 1. Water quality. ............................................................................................................................19 2. FPWF will stimulate recruitment, dispersal and spawning activity. .........................................20 3. Flows will maintain river character and behaviour. ................................................................20 4. Maintain waterhole habitats. ....................................................................................................20 5. Riffle habitats etc........................................................................................................................20 6. Maintain riparian habitats. ........................................................................................................21 8. Mean wet season flow volume will maintain a) estuarine productivity, and b) estuarine habitats...........................................................................................................................................22 9. Maintain Rare and/or Threatened species. ................................................................................22 Selection of indicators, methods of data collection, time frames. ................................................22 Indicator selection..........................................................................................................................22 Timing and frequency of sampling. ................................................................................................23
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Benthic metabolism. .......................................................................................................................23 Macroinvertebrate community structure........................................................................................24 Fish cohorts, community structure and fish movement. .................................................................24 Turtles. ...........................................................................................................................................25 Physical and chemical characteristics of in-stream habitats.........................................................26 Riparian habitat, vegetation community structure and canopy cover. ..........................................27 Frogs. .............................................................................................................................................28 Bird community structure...............................................................................................................28 Estuarine indicators. ......................................................................................................................29 Mangrove community structure. ....................................................................................................29 Physical characteristics and estuarine geomorphology. ...............................................................29 Projected Costings............................................................................................................................29 General observations/impressions ..................................................................................................29 Style etc. ............................................................................................................................................30 References. ........................................................................................................................................30

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PART ONE FITZROY BASIN RESOURCE OPERATION PLAN ECOLOGICAL MONITORING AND ASSESSMENT PROGRAM. PART 1 RESEARCH PROJECT BACKGROUND INFORMATION AND DESIGN Review by the Australian Centre for Tropical Freshwater Research, James Cook University
Introduction. The research project is the initial part of a long-term ecological performance monitoring and assessment program (p. 5) that is a statutory requirement of a Resource Operation Plan. It attempts to provide the means of assessing whether or not environmental flows (specified under the WRP [Water Resource Plan]) are achieving the desired ecological outcome. To meet this objective, a logical precursor is a sensitivity analysis of a range of indicators across a pre-defined gradient of alteration to the flow regime, forming the basis of protocols for monitoring the performance of the WRP. In the background information section (p. 6) it is stated that since the Fitzroy WRP was the first Plan prepared under the Water Act (2000), the outcomes for water management in particular, the security for environmental water requirements for aquatic ecosystems in the plan area were not explicitly specified. From a wider ecological perspective, it is evident that near-stream (riparian) communities and a myriad of dependent non-aquatic vertebrates that have been considered in other WRPs have been overlooked in this broad outcome as currently stipulated. This has been partly remedied by the study requirements (p.11) that aquatic vertebrates, in addition to fish, take into account amphibians, reptiles [presumably including those other than turtles, e.g. water dragon, Physignathus lesueuri and water skink, Eulamprus quoyi, where appropriate], water birds and monotremes [i.e. the platypus]. It is further stipulated that the study must address matters such as the condition of upper and in-channel riparian zones, floodplains and connected wetlands. The deliverables of this project are: 1) a set of appropriate indicators; 2) sampling methods for those indicators; 3) a sampling design that accommodates spatio-temporal variability and levels of confidence associated with impact detection; 4) an optimal sample number within accepted statistical error bounds; 5) an estimated individual indicator sample cost; and 6) the overall monitoring budget estimate. The purpose of the current review is to ascertain whether the methodology proposed is logically consistent, coherent and appropriate to the meeting of the stipulated objectives. Proposed research design. The extent of modification of Australian streams and their catchments has been well documented as part of the National Land and Water Resources Audit initiative of the Commonwealth Government in partnership with State and Territory agencies (Environment Australia, 2002). Most eastward draining streams exhibit moderate to substantial modification from their natural condition. In other words, impacts have already been sustained to varying, but often substantial, degrees. Accordingly, few if any sites within any major river system would offer conditions that might be regarded as a reference point from which departures from natural condition could be assessed. It is notable that this is accepted without empirical qualification as the essential justification for embarking on the nested gradient of impact approach. In fact, there is a clear deficiency in the citing of authoritative references throughout and mismatches of in-text references and bibliographic citations generally. Despite these deficiencies, the proposed design appears the most logical choice within this context. Nevertheless, despite lack of true replicate sites, inclusion of probable comparable sites from adjacent systems to help calibrate gradients more broadly might have been considered.
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The report rightly identifies problems associated with the type of assessment being attempted, which make the task difficult. Unfortunately, the report fails to address many issues that have to be included in consideration of flow influences. It also fails to provide sufficient details of methods, indicator measures, etc, to allow proper assessment. If the document is meant to be a summary of the approach, then full detail needs providing in appendices. And as a summary, the language is inappropriate as it would not be very intelligible to a lay person. These criticisms (which are intended to be constructive) are elucidated below. The choice of proposed experimental design is apparently forced upon the investigators as it is impossible to apply a conventional BACI style design because: (i) impacts have already been imposed (p. 13); (ii) appropriate controls are lacking (p. 14), and (iii) limited spatial scales of current Fitzroy IQQM nodes provide inadequate numbers of reference sites to employ spatial control procedures (p. 15). Whilst probably true, some evidence to support these assertions would have been useful (i.e., a table detailing the proportion of the basins streams of different order that have been regulated or a map showing the distribution of WRP nodes across the catchment). While the approach touted in Figure 4 may be the only one that comes close to being useable, there remains the problem of the underlying primary morphological, hydrological, physico-chemical and ecological upstream-downstream gradients, which may or may not be apparent within or between reaches [as is acknowledged on the next page]. We need to be convinced that there are no suitable reference sites somewhere across the catchment or in similar catchments. There should be discussion as to why sites in other catchments would be unsuitable as references, especially sites along longitudinal gradients the study might include investigation of this. In addition, references cited to support the use of gradient-type assessments are not listed in the bibliography, or are not listed in their entirety, or are not listed correctly, thus making any assessment of the merits of this approach exceedingly difficult. (N.B. over thirty references cited in the text are not listed in the bibliography and conversely, many references listed in the bibliography are not cited in the text). The underlying factor gradient variables might need to include ecological variables e.g. presence/absence of particular predators due to instream barriers may have a substantial effect on other measures. The report needs a map showing location of sites in relation to hydrogeomorphic features, and a table summarising site characteristics order, dimensions, flow, gradient, substratum, bank condition, etc. Note that reaches do not necessarily drain their adjacent landscape especially on floodplains, where drainage may reach the river further downstream via tributaries, or may enter completely separate drainages. This consideration needs to be explicitly included when determining the landuse characteristics of reaches. Few details with regard to site selection are set out in the document and as a result it is difficult to assess the validity of this component of the research design. It remains unclear as to how the selection of the 33 sites meets the theoretical principles of the ideal arrangement as set out in Figure 5. Moreover, it is specified that the long-term monitoring program will not be restricted to these sites (p. 16) but the extent of departure from the original site selection again is not specified. The lack of any spatial specifics distinctly hampers a critical review of this aspect of the program and the reader is left with the impression that gauging station distribution within the system (something which is likely to be associated with local physical attributes rather than synoptic physical variation within a given system) will be the major determinant of reach subdivision and monitoring site selection. Explanation of the characterisation of the flow regime pertaining to the various reaches (p 17) is also rather more general than specific. It is not explicitly stated how these flow data will be analysed or located along some notional gradient of disturbance or how any deviations from natural condition were established. Other concerns with regard to the derivation of a flow-disturbance gradient are associated with unspecified relative importance of individual indicator indices and the extent to which each may result in equivalent changes for each biotic component. Furthermore, if a multivariate
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approach was used to allocate sites to a disturbance gradient, it is vital to stipulate how this was achieved (cf. Auble et al. 1994, 1999). Similarly, some indication of the spread of sites across the three categories of flow modification (see Figure 4) would have assisted assessment of the proposed methodology. The incorporation of a gradient of disturbance consistent with varying land use categories is greatly reliant upon the work of Calvert et al. (2000). However, this citation is not listed in the bibliography and, as a result, it is very difficult to ascertain the veracity of this methodology of gradient ascription to this series of land use types (especially with regard to the highest level of potential impact being associated with a category specified as unknown uses [p.17]). Moreover, the level of resolution of the GIS data set and protocols for reach classification employing such data are not specified. This further constrains any critical review of the proposed approach. The notion of a landscape multimetric index (p.17) also does not appear consistent with the ascription of levels of potential impact to classes of land use types adjacent to individual reaches. Explanation of the ordination and vector plot using PATN (Figure 6) is unconvincing. Two objectives (one explicit, one implicit) of the study are given in the report. It is implied on page 5 that the objective of the study is .to assess the utility of a range of indicators in detecting a predefined gradient of alteration to the flow regime and it is stated on page 13 that the .. objective of the research project is to obtain the data necessary for addressing the design criteria used in subsequently establishing the Fitzroy long-term ecological performance monitoring and assessment programme.. Whilst these design criteria are not revealed, it seems reasonable to believe that they are related to cost effectiveness and efficacy in detecting flow-related impacts amidst myriad other impacts associated with land use. While, procedurally, performance may only need to be monitored when compliance is confirmed, it would be a sorry omission not to gauge performance at different levels of non-compliance (p. 6). Given that only six variables were used (p. 18), it would have been useful to plot a series of graphs to allow assessment of each of their patterns. Better consideration of the meaning of summed variables (which can be a very dodgy process) is required. It is difficult assessing the validity of the site selection process given the paucity of information presented to the reader and the lack of clarity in that presented (e.g., table numbering is out for the entire document). Specific points of concern with regard to the derivation of a flow disturbance gradient are: Although it is stated that flow data are available for 33 stations, it is not stated how these data are analysed or positioned along some gradient of disturbance. How were/are deviations away from natural for each flow parameter assessed? Was it similar to the benchmarking process used in other WRPs? Is each flow indicator assumed to be as important as another? For example, is a 15% deviation in the floodplain zone statistic equivalent to a 15% change in median annual flow? Are they expected to result in equivalent change for each biotic component? Is a multivariate approach used to allocate sites to a disturbance gradient? If so, how was it done? It is stated (p 17) that sites were selected from river sections with IQQM data, yet in the preceding sentences it is stated that IQQM data and gauged flows will be used. Have sites been selected or not? If sites have indeed been selected, why is a map not presented so that the potential confounding influences or natural gradients can be assessed? If sites have indeed been selected, some indication of the spread of sites across the flow gradient is required (i.e., a histogram). Are sites equally distributed across the three categories (highly modified, moderately modified and unmodified) depicted in Figure 4? In summary, the most important design criterion, flow regime change, is inadequately described.

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Land use impacts are better described, yet there are some concerns here also. Reliance on unlisted Calvert et al. (2000) noted above. Without this reference objective assessment of the methods strengths or weakness is impossible. Nevertheless, the process describing how a land use disturbance gradient is better explained than it was for flow disturbance. The disturbance gradient needs to be expressed in one dimension only (acknowledged on p. 18). How is a single index to be derived from the multivariate approach? Why isnt this process described? Why is there no indication of the distribution of sites along this gradient. Similarly, why isnt there some indication of the spread of sites of known disturbance throughout the catchment (i.e. a map)? Why is the final landuse multimetric score combined with a score for adjacent landuse type? Isnt the latter accommodated by the reach scale measures? What is the outcome of the event that ground truthing reveals substantial incongruity between ratings based on maps and local inspections? It is important that the simultaneous distribution of potential study sites along both gradients be assessed (i.e. a three-dimensional histogram). Are they equally spread along both gradients? If not, this will have substantial implications for analysis. Statistical methods. A nested gradient approach is appropriate for the kinds of investigations proposed here. However, some of the methods proposed above may prove difficult to accommodate within the design proposed. Throughout the document, there is a lack of information, or clarity in that information, as to what the predictions/hypotheses are and just what summary variables for each indicator are to be analysed. Much is made of statistics and power analysis, but there is little mention of the type of data to be fed in. Invertebrate community structure is a nebulous term for which there are various types of measure which will be used? Richness? Multivariate scores? What variables associated with the fish investigations are to be analysed: richness, relative abundances of specific fish, total biomass? Similarly, what variables are expected to arise from laparoscopic inspections? The document would have benefited greatly from the inclusion of a table, or amendment to Table 3, listing output parameters from each of the investigations, and expected types of change for each variable (i.e., some hypothesis concerning the relationship with the flow regime). It is imperative to know what statistical methodology is to be used prior to data collection, otherwise it may be found that the design is inappropriate. At present, the document almost suggests that CSIRO and CRC CZ are to be called in at the end to analyse a large mass of data. The analytical procedure apparently relies greatly on regression procedures. At present there is no mention of precisely how the analyses are to accommodate one gradient nested within another (particularly when both are numerical rather than categorical). Is partial correlation analysis to be used? Multiple regression? Has any thought been given to blocking sites along each gradient (such as indicated in Figure 4), so that ANOVA procedures (ANCOVA, nested ANOVA, nested MANOVA) can be used to examine relationships between indicators and flow regime changes? Would an ANOVA approach be more powerful than regression approaches, particularly when the form of relationships between indicators and disturbance gradients are unknown? This requires consideration. It is evident that four sampling trips are planned. How is the influence of different sampling occasions to be accommodated within a regression type approach? It is not clear how (c), p 21, will identify confounding natural gradients. Ecological Goals and Hypotheses (Table 3 etc.) The tabular presentation of indicators and methods is a good idea, but is currently inadequate. Examples of why are listed below. Each goal, hypothesis and indicator requires reworking to address
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the sort of issues raised. It would be expected that Table 3 would detail the measures associated with the indicators e.g. fish community structure might be described in a number of ways how will it be used here? How are fish larvae an indicator? Without such indication it is not possible to assess the validity of the methods. The impression at this stage is of a shot-gun approach that has not been adequately thought through. This may be untrue, but it is what the evidence suggests. 1. Water quality. A proper discussion of water quality issues is required, providing the basis for a fully elucidated water quality sampling design. For example, release of water may artificially improve water quality where it would otherwise have deteriorated naturally. Diel (or dawn/dusk) sampling is critical for DO and pH assessments, which may be greatly affected by flow regime. They are also greatly affected by the biomass of macrophytes (as are nutrients). DO, pH and nutrient measures may be next to useless without estimates of plant biomass (which dont appear to be included in the program). How will flow affect turnover? How will this be monitored? The proposed sampling frequency will not help sort this out. 2. FPWF will stimulate recruitment, dispersal and spawning activity. The hypothesis that the first post-winter flood will achieve all these important functions with respect to fish assemblages relies largely on anecdotal data in Merrick and Schmida (1984), selective quotation of material in Pusey et al (1999) (for example, the inference that increased spawning in Mogurnda adspersa occurs when water temperatures are elevated (Table 4) ignores the suggestion in Pusey et al. (1999) that northern populations of this species spawn in spring) and appears to be uncritically derived from the Arthington et al. (1992) explanation of the holistic approach. It must be noted that many fishes spawn during periods of low flow during the spring months. The FPWF may be detrimental to recruitment in these species if it occurs in October or November (i.e. it may be a source of mortality). Similarly, for those species that spawn during summer, is flood occurring in April likely to affect reproductive success as one occurring in February? Given that the pilot study is expected to last for two years only, these concerns are unlikely to be addressed properly. The likelihood that the FPWF will maintain reproductive processes and movement of native flora & fauna (p. 24) in the riparian system is arguable. In light of (i) the general lack of knowledge of plant phenologies and precise triggers to phenological events, (ii) the great structural and floristic variation in these communities, and (iii) different species being differently stimulated, it is unlikely that there would be any candidate indicator. 3. Flows will maintain river character and behaviour. Whilst the hypothesis is reasonable, it is questionable whether the study can fully address this issue in its short time frame. It is not stated in the design particulars the length of time that reaches have been subjected to flow modification. Geomorphological responses to altered flow patterns typically take many years to become evident and any design proposing to define the extent to which flow manipulation impacts on channel structure must be mindful of the long time scales involved. Mapping would have to include variables such as soil type, which may confound other measures. 4. Maintain waterhole habitats. Certainly, this is a reasonable goal. Water holes can be vulnerable to altered flows (whether reduced or supplemented). We need to understand their seasonal dynamics degree of flushing, stratification, water quality diel cycling and seasonal changes, etc. Macrophytes may be an important component of the biota (and a major influence on water quality) and should be included in all assessments. 5. Riffle habitats etc. Maintaining riffle habitats may be a sensible goal if such habitats are permanent, but not if they would naturally dry, as often happens in such systems (this consideration may be incorporated within the
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natural variability). Again, understanding their natural dynamics is important for goal setting under altered flows. 6. Maintain riparian habitats It is clear that flows in natural waterways are associated with responses in both the in-stream and nearstream communities. To date, attention has been focussed on detecting the relationships between flow regulation and in-stream assemblages particularly of freshwater fishes (Bowen et al. 1998, Hughes et al. 1998) and aquatic macroinvertebrates (Fore et al. 1996, Smith et al. 1999). Investigation of the impacts of flow regulation on other in-stream communities such as the aquatic macrophytes (eg, Small et al. 1996) also appears to be in its early stages, and, apart from the work of Mackay and Thompson (1999), largely confined to those of northern hemisphere temperate streams, particularly in France (Bornette and Amoros 1991, 1996; Bornette et al. 1998). Impacts on the near-stream vegetation communities, however, seem to have received less attention and predictions are more reliant on generalisation and supposition. Despite this work has been conducted in an attempt to elucidate the connection of riparian vegetation to stream flows. Nilsson et al. (1997:798) have documented the long-term responses of river margin vegetation in central Sweden to water level regulation and confirm that riparian ecosystems provide clear indications of environmental change. Because of its close dependence on streamflow, riparian vegetation can be very sensitive to changes associated with water development (Auble et al. 1999) and, therefore, provide reliable indicators of impact. In Australia, there is ample evidence for the decline of riverine and riparian vegetation along the River Murray being related to flow regulation (Walker 1993:33), and there is evidence of dieback due to irrigation-induced waterlogging in the Burdekin floodplain. Walker and Thoms (1993) document such a decline as beginning in the 1930s but expanding greatly in the 1950s and provide some understanding of this impact. Explicit consideration of the coupling of components of annual stream flow hydrographs and the germination of certain riparian species can be found in Shafroth et al. (1998). This work, conducted along streams in Arizona, identified key hydrograph components including (i) timing and magnitude of flood peaks, (ii) rate of recession of the falling limb of the hydrograph, and (iii) the magnitude of base flows, that greatly influence seedling germination and, eventually, successful establishment. These results, based on four riparian species (3 native and 1 exotic), were considered to be generally applicable to other woody species in the riparian zone. Thus, despite obvious problems due to the complexity of near-stream systems and the lack of a large literature on links with stream flows, there have been some investigations. However, there is little within the draft document to suggest that there is an appropriate understanding of that literature and how research findings might be incorporated into monitoring programs. Note that riparian indicators will be substantially affected by land use and degree of disturbance due to stock, weeds, fire etc. How will these variables be incorporated? 7. High flows will provide natural connectivity between watercourses and associated floodplain and wetland habitats to support natural flora and fauna. It is not immediately clear what is meant by natural connectivity in this hypothesis, or what indices are logically indicative of this important ecological process. Presumably, it refers to maintaining natural levels of inundation, frequency of inundation each year, length of inundation per spell, timing of inundation spell and not just the extent of inundation (i.e., wetted area). It is not clear whether all of these parameters can be estimated from satellite imagery (are images taken frequently enough, for example?). It may be appropriate to use standard hydrological and geomorphological techniques to model floodplain inundation extent and estimate spell lengths and frequencies by relating discharge, stage height and channel geometry and truthing these predictions against satellite imagery. It may prove difficult to accommodate this hypothesis within the nested gradient approach given that not all sites are likely to have associated floodplains or wetlands. The time frame necessary to understand the dynamics of these systems may reduce utility of the indicators. Indicators should include macrophytes as a key to water quality processes, habitat and ecological processes. What is meant by bird
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community structure simply the species list? Abundance of species? Or interrelationships in the food web (which incorporates more of the notion of structure than richness and abundance). The obvious birds can have limited value as indicators as they can be transient; this is especially true with a limited sampling frequency. With regard to riparian communities, appropriate indices might be obtained from various existing studies that are not cited. Many focus on the extent and longevity of water level changes. The early work of Franz and Bazzaz (1977) that related the occurrence of riparian trees to inundation duration and that of Harris et al. (1985) that employed hydraulic simulation models to describe plant distributions along transects orthogonal to the stream channel would have provided useful models. These studies provide the foundation for the approach which links the present distribution of different cover types of riparian vegetation to inundation duration as derived from flow-duration curves. Instream dams or diversions have predictable influences on the flow duration curve and can be used in combination with gradient analysis to predict impacts. Inundation duration integrates or is correlated with flow-related variation in a range of variables such as shear stress, sediment deposition and erosion, depth to groundwater and to soil oxygen concentrations experienced in the riparian zone such that it has considerable potential as a predictor of vegetational change. Other multivariate measures associated with the impact of water level fluctuation might have been obtained from the more recent Australian work of Brownlow et al. (1994). 8. Mean wet season flow volume will maintain a) estuarine productivity, and b) estuarine habitats. Much of the eastern Australian data concerning fisheries catches and wet season flows do show a positive relationship between the two. However, the hypothesis as stated infers that this relationship is solely due to an effect on productivity (i.e. greater fisheries catches = greater productivity). This may not always be so as, in some cases, greater catches result from increased mobility and hence catchability associated with high flows. In some instances the opposite occurs. The hypothesis that estuarine habitats are dependent only on wet season flows ignores the other half of the year. The water quality measures need elucidating water quality cannot be applied as a simple catch-all. Each variable is complex, and can be even more so in estuaries, where tides, salinity, wind, etc. may have major influence. 9. Maintain R&T species. Ensure that the proposed monitoring does not adversely affect these species! While it may be difficult to ascribe changes in R&T populations to flow (or anything else), especially if population densities are very low, it is worthwhile monitoring the populations in any case. The exclusive focus on Rheodytes leukops (note that the species name is inaccurate in the draft text) is insufficient. While this endemic turtle is of very high conservation significance, the program should include other near- or in-stream plants and animal species. Elements of the flow regime other than base flow (e.g. first flushing flows and high flows) may have implications for rare and/or threatened species at particular stages of their life cycle (especially reproduction). Selection of indicators, methods of data collection, time frames. Indicator selection. It is clear that a great range of candidate indicators and metrics have been investigated as surrogates for water quality, but the absence of specifics and simple reference to the TAP and Storey & Smith, 2001 (which does not appear in the bibliography and is useless to this review) is inadequate. Timing and frequency of sampling. This is always a compromise between the desirable and the affordable. Biannual sampling will be adequate for the purpose for some measures, but not for others, where understanding of daily and/or seasonal dynamics is required (as indicated above). In some cases, event-based monitoring is important, while for others, avoiding events (especially floods) is important. Events may be postAustralian Centre for Tropical Freshwater Research Page 7

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flood or minimum flow periods. Knowledge of antecedent conditions is critical, and appraisal of this should be explicitly included. Fully critical appraisal of timing against each measure is required. Benthic metabolism. The incorporation of studies on benthic metabolism in an investigation of the effects of flow modification is laudable as even small changes in carbon production may translate into substantial effects in other parts of the food web. However, the process by which benthic metabolism will be incorporated into the design is not made clear. For example: nowhere is it stated how many replicate chambers are to be installed at each site on each occasion; it is not stated whether domes are to be positioned across all different habitat types or is sampling intended to be stratified? how are changes in GPP and R24 values expected to change with differing levels of flow regime impact? as the domes are bottomless, some indication of their sensitivity to exchange in the substratum, and effects of different substrata, is required; there is no indication of what hypotheses are to be tested concerning flow manipulation and benthic metabolism; how will the impacts of antecedent flows be accommodated within the study design given the small number of sampling occasions? For example, elevated flows occurring a short time prior to sampling may have disturbed existing micro-algae or redistributed detritus. How are such effects to be considered? the construction and deployment of the domes is no easy task will it be done in-house or contracted out? The budget is insufficient for the latter. Does sufficient expertise exist within the team? Insufficient information is given to allow assessment of this component (the reference to Bunn et al. is inadequate). These concerns relate to the extent to which benthic metabolism can be related to discharge manipulation. Consider the example where flow manipulation results in an increase in available habitat across which some habitat patches, although limited in extent, become greatly autotrophic, whereas other patches remain heterotrophic. How is it intended to accommodate such effects? Macroinvertebrate community structure. While the AusRivAS methodology may be appropriate, a proper description of how it will be applied, and a critical appraisal of it (e.g. arguments about effects of inclusion or exclusion of rare taxa) are required. It is assumed that by structure, it is composition (including relative abundance) that is actually meant, as structure implies functional links that are not a component of the study. Studies of fish in the Fitzroy are reviewed, but not of the invertebrates why? An explanation of the sample design and techniques is required. For example, at what depths will water holes be sampled? What sampling devices will be used? Will macrophytes be included? How will different substrata be incorporated? Are riffles permanent (it is not clear from the report)? For the wetlands, we need to have more information on how macrophytes might be included. How will samples be quantified? How many replicates per habitat, per substratum, per macrophyte species? Fish cohorts, community structure and fish movement. Table 4 does not appear to be referred to in the text, and is in any case out of place in this document. The sampling methodology proposed to collect fishes is, in general, adequate providing that the following concerns are addressed: The sampling protocol developed by Pusey et al. (1998) is intended for use in streams and rivers with depths less than about 1 m. It is inappropriate to employ this method elsewhere, such as in water holes. The extent to which the QDPI sampling methods address this problem is unknown as no details or reference are supplied. Water holes are apparently of great
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significance in the Fitzroy River, yet no method for sampling fishes in these habitats is described. The sampling protocol of Pusey et al. (1998) is intended to supply quantitative data on fish density and biomass. Other methods currently employed in Queensland provide data only in terms of catch per unit effort. What are the expected units in the proposed study? What are the indicator metrics species richness, biomass, density? It is stated (p. 30) that individual hydraulic units in each site will be sampled and then data pooled. This approach is analytically appropriate only when all sites contain the same array of hydraulic unit habitat types. The analysis would be much more powerful if it were stratified to accommodate between-site differences in habitat availability and extent. The same concern applies to the use of supplementary seine netting. There is comment (p. 37) on the need for rare and threatened species requiring particular attention. However, nowhere in the document is any mention made of fish species of high conservation status. The Fitzroy River contains one endemic species (Saratoga), one endemic subspecies (Yellowbelly) and another species of limited distribution (Leathery grunter). The first two species are of recreational fishing significance. Surprisingly, no mention is made of these species (other than in Table 4). Yellowbelly and Leathery grunter both make flowrelated spawning migrations and are thus likely to be affected by flow regulation. Saratoga spawn during spring and are thus likely to be negatively affected by an early FPWF. No measures are suggested that would allow an examination of the impacts of flow regulation on these species. Note that larval sampling is unlikely to collect any of these species because (i) Saratoga are mouth brooders, and (ii) potadromous spawners that make large migrations and produce pelagic eggs do not produce many pelagic larva that can be sampled for example, Humphries and colleagues have failed over many years to collect a single Yellowbelly larva by conventional passive sampling means. The proposed design includes provision for larval fish sampling but the authors also state that larval fish sampling will not be continued in the final monitoring program, rather some supposed relationships between juvenile cohort size and age/length relationships yet to be developed by a student under a yet to be confirmed supervisor will be used to examine the impact of flow regulation. The authors correctly note that flow regulation might depress recruitment by removing conditions necessary to stimulate spawning, or failing to sustain those larvae produced. The proposed juvenile recruitment method will not allow an objective assessment of the extent to which either of these two factors contribute to any recruitment failure that may develop. [NB see note below about student projects and appropriate supervision.] It is stated that larval fish abundance will not be used to examine flow/recruitment relationships. Rather, presence/absence will be the indicator of choice. Many species of fish produce small numbers of larvae year-round although most larval production occurs during more well-defined periods, which may or may not be related to flow regime (see Pusey et al. 2001). A presence/absence approach will not be useful with respect to these species, which probably make up the bulk of fishes present. Therefore, this approach will be unlikely to provide any meaningful assessment of the impacts of flow regulation. Cohort analysis relies on the presence of distinguishable cohorts. This is often very difficult in Queensland fish populations due to prolonged breeding seasons and variability of flow. How will this be accommodated in the design? It is stated that some larval fishes are difficult to identify. How will this overcome? None of the hypotheses concerning flow/fish were generated using data from the Fitzroy River (noting that this river is apparently one of the most variable in the world). Are the hypotheses appropriate? Fish movement is not addressed anywhere yet is a critical component of any program addressing the effects of flow regulation on fishes. What would be the purpose of estimating fish weight from length measurements if one is directly correlated with the other? Would real weights be useful to show deviation from the relationship, indicating condition? Student project supervisor should be someone with knowledge of Australian fresh waters and freshwater fish. Questionable whether it is appropriate to depend on a student project (although great value could be added by having non-essential projects attached to the study).
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Turtles. Turtles are a significant vertebrate component of any Queensland river and the inclusion of this taxon is appropriate. However, whilst acknowledging the high conservation status of R. leucops, the program should be expanded to include other species, particularly as they will be collected at the same time as R. leucops (p. 38). It is assumed that discussions have been held with appropriate turtle researchers such as Col Lympus and the proposed collecting regime may be the most effective, although dismissal of funnel trapping maybe too hasty would it not be worth trialling the method? But, while monitoring turtles is appropriate, are they likely to be useful as indicators? Are the investigators able to distinguish different turtles species at night under spotlighting conditions? The principal concern with the method is that it may prove difficult to incorporate the collecting data into a valid statistical analysis. Other concerns include: It is not clear why turtles are tagged upon capture. Are the investigators intending to estimate population sizes (by mark recapture techniques), estimate growth, estimate habitat use or movement patterns? Some discussion of the methods proposed if any or all are intended would be useful. It is unclear how laparoscopic investigation can provide the data stated, but more importantly, it is unclear which personnel are to perform this examination. Presumably substantial expertise is required to ascertain breeding status does this expertise already reside in the project team? From the budget/costing details presented on pages 44 & 45 (i.e. $99.25/site), it is assumed that outside consultants will not be used. However, the stated method suggests at least 4 person/hours of snorkelling, plus some undefined period of spotlighting, plus laparoscopic investigation, plus location, inspection and measurement of nesting sites will be required. How can this be achieved for only $99 per site? How are data on nest location, fox activity, breeding biology intended to be analysed? Physical and chemical characteristics of in-stream habitats. There appear to be some misconceptions about habitat structure and its measurement. For example, the IFIM approach does not assess the condition of water resources (it models habitat responses to varying discharge) (p 38), and quantification of the amount of habitat does not necessarily allow a surrogate measure of the potential abundances of biological communities. This point assumes that habitat availability is the limiting resource. The authors correctly identify that aquatic habitat needs to be considered at a variety of scales, yet the proposed sampling regime does not facilitate such an examination. The SoR approach was designed to allow an assessment of river condition; it was not designed for complex habitat mapping nor does it yield data amenable to statistical examination in the design proposed here. Information of habitat structure (flow, depth, substrate composition, the presence of woody debris etc) needs to be collected within a random points design involving substantial replication. Other important points: The intention of the cross-sectional surveying is not immediately clear. It appears that it is required to explore indicator criteria for both river geomorphology and waterhole structure. Given the difference in scales, both spatial and temporal, can the same method be used for both? It is not clear how cross-sections will be related to flows given the possible confounding criteria such as soil type, gradient, vegetation, etc. Explain how transect positions will be located on subsequent sampling occasions. Will the limited temporal examination allow seasonal differences in habitat structure to be fully appreciated? How are antecedent flow events accommodated? Why are velocity and depth the only variables to be measured along each transect? Why not substrate composition, presence of macrophytes, woody debris? All are expected to varying according to flow regime.
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Throughout the document, emphasis is placed on two important habitat types, namely riffles and water holes (pools). It is possible that a single surveying/mapping methodology may not be achievable. Two water quality variables (temperature and DO) are to be measured. Presumably these variable are important as indicators for deteriorating water quality in waterholes. However, this seems to be a very sparse assessment of water quality. It is therefore assumed that other water quality variables are measured. However, no details about which parameters are to be measure are given. Are nutrients to be measured? Pesticides? What variables will allow land use effects to be factored out in the final analyses? How will DO, pH be related to macrophytes (which dont appear to be included)? A water quality sampling design is required, addressing the above points and other issues such as diel (or dawn/dusk) sampling critical for DO and pH, both of which may be greatly affected by flow regime. Is turbidity to be measured? This will be of great relevance to benthic metabolism, and may be important in determining the distribution of R. leukops (Cann, 1998:239). Note other problems with water quality assessment, discussed above.

It must be stressed that habitat structure (including aquatic plants) may have substantial consequences in determining the presence/absence of particular species, their abundance (under special circumstances), condition and reproductive success. It is therefore critical that habitat structure (including dispersal barriers) be quantified so that it may be meaningfully incorporated in the statistical analysis. Note that costings for geomorphological examinations are not included in Table 6 (although they are for Table 5). Riparian habitat, vegetation community structure and canopy cover. How useful is riparian vegetation as an indicator in the short term, given that responses to changed flow regimes may take years to be measurable? It is apparent here that there is some understanding of the functional importance of the near-stream communities and of the utility of incorporating these components into metrics used to assess stream health. Recognition that the often poor condition of the riparian verge is due to non-water resource related factors (especially clearing, uncontrolled stock access and exotic species invasions) is clearly warranted at the outset, as these factors greatly confound the exercise of teasing out impacts on the riparian zone that are flow-related. The SoR approach to be adopted, while generally appropriate for an assessment of gross condition, appears largely inadequate within a nested gradient approach to the determination and monitoring of flow-related impacts on this component. While the author of the SoR assessment method to be adopted himself claims that the derivation of a single variable or index of riparian condition is an impossible task (Anderson 1993:15), the use of a rating system to combine several attributes is most reliant upon observer standardisation and relies also upon botanical knowledge on the part of an observer or monitoring team to identify major species and to discriminate between native and exotic species. These can be inadequacies already detectable in SoR data sets and it is an issue that is distinctly relevant to data interpretability and should have been raised as part of a detailed proposed methodology. While single scores (usually ranked or ordinal), however derived, can tell us a great deal, they are difficult to interpret in isolation and without the application of considerable expertise. There is also a need to clarify the notion of a vegetation scaling factor that relates to vegetation density (p. 39). Anderson (1993:97) does state that his method of riparian vegetation condition assessment employs a combination of the reduced cover compared with a regional or catchment standard, but due to the degree of modification of the riparian zone previously alluded to, such standards may well be elusive. This is an issue that deserves some consideration. There are some misconceptions evident in the wording of the draft text. Presumably FPC refers to projective foliage cover (more properly PFC) as a conventional attribute in Australian vegetation
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structural classificatory systems rather than foliage protection cover. Such simple errors of translation of existing vegetation science protocols do not instil confidence in the study. The assessment of a 100-metre section of both banks rather than a narrower (or undefined) swathe at 25 metre intervals is preferable to a single transect at a given site, however, my experience leads me to believe that the inherent variability within riparian communities will not be comprehensively captured. First-hand experience in the Pioneer and Proserpine River systems indicates that a significant time allocation at each reach is required to undertake such survey accurately and comprehensively. In addition, there is still no way the representativeness of the sample can be adequately determined without much greater effort to ascertain this from more synoptic aerial photographic coverage or by some other means. Aspect, in many instances, is a major determinant of riparian zone structure and floristic make-up. This has not been adequately addressed in any of the dedicated methodologies yet derived. Moreover, no detail is provided as to how evidence of regrowth, dieback and other indications of disturbance (p. 40) will be recorded. There are, of course, some standard forestry mensuration techniques available to which reference might have been made. Frogs. The proposed focus on frogs as an indicator group is laudable but fraught with problems. While often sensitive to environmental changes because of their permeable skin that makes them closely link with the ambient environment, frogs are also a diverse group of organisms. Some are highly reliant upon access to access to wetland breeding sites while others are obligate lotic stream dwellers, and others still do not possess a free-living tadpole stage and instead are reliant upon access to a moist leaf litter substrate. It is not clear how the sampling design for frog data collection might be related to flow regime. Frogs are indeed difficult to incorporate in monitoring programs (p. 41) and the authors suggest that automated recorders are the most appropriate way of broad-scale sampling. Such a sampling technique, if employed regular intervals at appropriate sites (e.g. a reliable wetland where frogs aggregate to breed) and the most appropriate time during the year (and this may well not coincide with the two proposed sample periods i.e. (i) March-June at the end of the wet season; or (ii) SeptemberDecember at the end of the dry season) can provide local or district trends in frog assemblage composition and relative species abundances. These trends, however, are unlikely to be directly related to flow changes in a river system but to broader climatic oscillations and/or land uses surrounding a strategic wetland, and certainly could not be confidently interpreted as reliably representative of this group. Automated recording of singing males can only be used to determine species richness of frogs at a particular site and is not wholly appropriate for measuring abundance, unless sampling intervals approximate the repetition rate of individual species (Heyer et al. 1993) or call intensity is somehow averaged over time, and overall intensity is used as a surrogate for abundance. It is not recommended for comparing different sites or for species with explosive breeding cycles. Given these constraints, it may prove difficult to monitor frogs. However, in view of the substantial difficulties in incorporating frogs into rapid assessment protocols using other methods, it is considered worthwhile to trial this methodology. Bird community structure. The inclusion of birds in the program is valid as many species can be reliant upon the integrity of riparian zones and can be a useful indicator group. However, different species exhibit very different associations with water bodies: some are sedentary residents, others seasonal (including international) migrants, while others (e.g., honeyeaters) are very irruptive or nomadic. Additionally, impacts on the riparian zone may not show up for several years. It will therefore be difficult to demonstrate any effect of flow regulation on bird communities. However, it would be useful to develop a standard system through which a subset of the bird community might be reliably linked to flow regime change, for this and other WRP areas. The collaborative venture with Griffith University will add value to the project, although it will be unlikely to contribute directly to it within its own time frame.

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Estuarine indicators. The proposed estuarine methodology is weak. Is it possible to include other estuaries as benchmarks? Or as part of a gradient? The possibility needs discussion, even if it is not viable. The time required to be able to link any measures to flow variation is likely to be unacceptably long. Reference to outputs of the CRC project is not adequate the methodology should be described if it is to be adequately assessed. The same applies to assessment of mangroves and physical characteristics. How would other cumulative effects of long-term changes be factored out? Note that end of system indicators such as the size of the annual fisheries catches are usually associated with the volume of stream flow rather than the flow regime. Mangrove community structure. The investigation of trends in the relative cover of this community type from historical aerial photographic interpretation is a standard and reliable technique. The linkage between mangrove cover and flow regimes is less well understood. Given the opportunity to involve some specialist investigation of this component, its inclusion is a positive aspect of this draft proposed program. Physical characteristics and estuarine geomorphology. The above comments apply similarly here. Projected Costings. It is difficult to comment on the budget without at detailed, itemised design to justify it (sites, replicates, etc). It is surprising that the birds cost more than the bugs, given the processing time for the invertebrates. General observations/impressions. The draft proposal clearly needs much work to produce an adequately detailed and justified monitoring program. In addition, there are some obvious misconceptions in relation to some biological components that warrant attention. There also appears to be a lack of review of the many techniques that are available or have been trialled and which might have been assessed with regard to their utility. There is a distinct lack of detail in those protocols proposed that constitutes a major shortcoming. Questions as to how the investigation will be practically undertaken, and at what sites at what locations and how will the various sites be accommodated across multiple environmental gradients continually arise. The possibility of confounding effects is recognised, but such effects are not properly detailed. There are, however, some positive signs within the document. The adoption of a nested gradient approach is a logical step to ascertaining flow-related impacts on an array of ecosystem components within a complex landscape context. This is so despite the scientific techniques being difficult to apply in the field and often awkward to interpret with regard to the major objective of such a research program. Opportunities to collaborate with specialists have also been taken and will add value to the research program. Unfortunately, the need for observer standardisation and some specialist biological knowledge is not identifiably addressed and may pose considerable difficulties for program implementation. Style etc. There are problems with use of tense throughout the document. It appears that this may have arisen from cutting and pasting from other documents without subsequent editorial checking. This may also explain the problems with reference citation. There are errors of nomenclature, in table referencing, and many omissions from the bibliography that severely constrain this review process.
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The writing is reasonably clear, at a technical level, but the informed layperson would find the going tough. Some rules are broken: e.g., never put a semi-colon after and it performs like a full-stop. And dont use the semi-colon to introduce a list or an idea: the colon is the correct mark (as here). Use semi-colons to separate clauses of equal weight (as here); and use them to separate items in complicated lists (as has been done in some cases). One or two sentences lack verbs, theres mixing up of effect and affect, and other minor misdemeanours. Nothing that an experienced proof-reader couldnt correct.

PART TWO FITZROY BASIN RESOURCE OPERATION PLAN ECOLOGICAL MONITORING AND ASSESSMENT PROGRAM. PART 1 RESEARCH PROJECT BACKGROUND INFORMATION AND DESIGN
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Review by the Australian Centre for Tropical Freshwater Research, James Cook University Preamble to 2nd draft, September 1, 2002 This second version of our review includes responses to the draft review from the authors of the research project, and some additional comment from the review team. Summary responses from the project authors are included as footnotes to the review, and additional comment from the reviewers is then given in the footnote in italics. The original review was replete with criticisms, but this does not mean that we deny that there are difficulties associated with the problem to be addressed, and that they are not necessarily of the authors making. However, every weakness in the proposed methodology must be properly elucidated, so that the likelihood of unequivocal outcomes can be assessed. What is the sensitivity of the methodology to various types and levels of weakness? Will patterns be so confounding that nothing will be discernible, thereby undermining the whole process? We hope not but such issues must be addressed. It would be better to indicate the level of confidence in the likelihood of an outcome now, rather than spend a lot of money and time coming up with an equivocal and challengeable result. The responses of the authors to the review are mostly constructive, although there is some testiness apparent at times, and there has been selectivity in the criticisms addressed there are many queries or criticisms that were not addressed (and so do not have a footnote associated with them). We acknowledge that it is easy for a reviewer to criticise. But that is our job, and criticisms do need addressing, whether they be of the proposal or flaws in the brief or other advice. Note that even though a TAP might have decided something, or a brief requires something, a consultant should apply their expertise to advise the client if the brief is too restricted, or if precepts are flawed. The authors occasionally dismiss difficult problems as being not in the brief, or being a result of the TAPs determination, and so they are stuck with it. We reviewers are not stuck with it, and the points still need addressing. We should state clearly here that we believe the approach taken by the proposal is essentially correct, in that it is the best option available in the real world. Our substantive criticisms do not undermine this process, but do point to difficulties that are readily addressable or alternatively need to be explicitly articulated to provide a comprehensive understanding of the context of the study, its outcomes, and its limitations. We have taken the opportunity to undertake some minor editing to tidy up the document. We appreciate that there may be some repetition in this review. Introduction. The research project is the initial part of a long-term ecological performance monitoring and assessment program (p. 5) that is a statutory requirement of a Resource Operation Plan. It attempts to provide the means of assessing whether or not environmental flows (specified under the WRP [Water Resource Plan]) are achieving the desired ecological outcome. To meet this objective, a logical precursor is a sensitivity analysis of a range of indicators across a pre-defined gradient of alteration to the flow regime, forming the basis of protocols for monitoring the performance of the WRP. In the background information section (p. 6) it is stated that since the Fitzroy WRP was the first Plan prepared under the Water Act (2000), the outcomes for water management in particular, the security for environmental water requirements for aquatic ecosystems in the plan area were not explicitly specified. From a wider ecological perspective, it is evident that near-stream (riparian) communities and a myriad of dependent non-aquatic vertebrates that have been considered in other WRPs have been overlooked in this broad outcome as currently stipulated. This has been partly remedied by the study requirements (p.11) that aquatic vertebrates, in addition to fish, take into account amphibians, reptiles [presumably including those other than turtles, e.g. water dragon, Physignathus lesueuri and water skink, Eulamprus quoyi, where appropriate], water birds and monotremes [i.e. the platypus]. It is further stipulated that the study must address matters such as the condition of upper and in-channel riparian zones, floodplains and connected wetlands.
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The deliverables of this project are: 7) a set of appropriate indicators; 8) sampling methods for those indicators; 9) a sampling design that accommodates spatio-temporal variability and levels of confidence associated with impact detection; 10) an optimal sample number within accepted statistical error bounds; 11) an estimated individual indicator sample cost; and 12) the overall monitoring budget estimate. The purpose of the current review is to ascertain whether the methodology proposed is logically consistent, coherent and appropriate to the meeting of the stipulated objectives. 1 Proposed research design. The extent of modification of Australian streams and their catchments has been well documented as part of the National Land and Water Resources Audit initiative of the Commonwealth Government in partnership with State and Territory agencies (Environment Australia, 2002). Most eastward draining streams exhibit moderate to substantial modification from their natural condition. In other words, impacts have already been sustained to varying, and often substantial, degrees. Accordingly, few, if any, sites within any major river system would offer conditions that might be regarded as a reference point from which departures from natural condition could be assessed. It is notable that this is accepted without empirical qualification as the essential justification for embarking on the nested gradient of impact approach. Here and elsewhere, there is a clear deficiency in the citing of authoritative references and there are mismatches of in-text references and bibliographic citations generally. Despite these deficiencies 2 , the proposed design appears the most logical choice within this context. Nevertheless, despite lack of true replicate sites, inclusion of probable comparable sites from adjacent systems to help calibrate gradients more broadly might have been considered. Unfortunately, the report fails to address many issues that have to be included in consideration of flow influences and it fails to provide sufficient details of methods, indicator measures, etc, to allow proper assessment. If the document is meant to be a summary of the approach, then full detail needs providing in appendices. And as a summary, the language is inappropriate as it would not be very intelligible to a lay person. These criticisms (which are intended to be constructive) are elucidated below. The investigators indicate that the choice of experimental design was forced upon them as it was impossible to apply a conventional BACI (before-after-control-impact) design because: (i) impacts have already occurred; (ii) appropriate controls are lacking, and (iii) the current Fitzroy IQQM nodes provide inadequate numbers of reference sites to employ spatial control procedures. Whilst these factors are not disputed, some evidence to support them was warranted (e.g., a table detailing the proportion of the basins streams of different order that have been regulated or a map showing the distribution of WRP nodes across the catchment). While the approach outlined in Figure 4 may be the only one that comes close to being useable, there remains the problem of the underlying primary morphological, hydrological, physico-chemical and ecological upstream-downstream gradients, which may or may not be apparent within or between reaches [as the authors acknowledge later]. We need to be convinced that there are no suitable reference sites somewhere across the catchment or in similar catchments. There should be discussion as to why sites in other catchments would be unsuitable as references, especially sites along longitudinal gradients the study might include investigation of this. 3 References cited to support the use of gradient-type assessments are incompletely listed in the bibliography, making any assessment of the merits of this approach exceedingly difficult. 4 The underlying factor gradient variables might

The proponents state that confusion over project objectives has been addressed combine separate statements to form a clear single objective. 2 Acknowledged by authors, and to be addressed. 3 The proponents have supplied further justification of approach supplied and have stressed that there will be sufficient reference sites for the approach to work. The response indicates that the team is aware of the difficulties and has strategies to address them. 4 Bibliographic problems acknowledged to be addressed and bibliography made complete in final document.
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need to include ecological variables e.g. presence/absence of particular predators due to instream barriers may have a substantial effect on other measures. The report needs a map showing location of sites in relation to hydrogeomorphic features, and a table summarising site characteristics order, dimensions, flow, gradient, substratum, bank condition, etc. Note that reaches do not necessarily drain their adjacent landscape especially on floodplains, where drainage may reach the river further downstream via tributaries, or may enter completely separate drainages. This consideration needs to be explicitly included when determining the landuse characteristics of reaches. 5 Few details with regard to site selection are set out in the document and as a result it is difficult to assess the validity of this component of the research design. It remains unclear as to how the selection of the 33 sites meets the theoretical principles of the ideal arrangement as set out in Figure 5. Moreover, it is specified that the long-term monitoring program will not be restricted to these sites (p. 16) but the extent of departure from the original site selection again is not specified. The lack of detail regarding site locations distinctly hampers a critical review of this aspect of the program and the reader is left with the impression that gauging station distribution within the system (something which is likely to be associated with local physical attributes rather than synoptic physical variation within a given system) will be the major determinant of reach subdivision and monitoring site selection. 6, 7 Explanation of the characterisation of the flow regime pertaining to the various reaches (p 17) is also rather more general than specific. It is not explicitly stated how these flow data will be analysed or located along some notional gradient of disturbance or how any deviations from natural condition were established. Other concerns with regard to the derivation of a flow-disturbance gradient are associated with unspecified relative importance of individual indicator indices and the extent to which each may result in equivalent changes for each biotic component. Furthermore, if a multivariate approach was used to allocate sites to a disturbance gradient, it is vital to stipulate how this was achieved (cf. Auble et al. 1994, 1999). Similarly, some indication of the spread of sites across the three categories of flow modification (Figure 4) would have assisted assessment of the proposed methodology. 8 The incorporation of a gradient of disturbance consistent with varying land use categories is greatly reliant upon the work of Calvert et al. (2000). However, this citation is not listed in the bibliography and, as a result, it is very difficult to ascertain the veracity of this methodology of gradient ascription to this series of land use types (especially with regard to the highest level of potential impact being associated with a category specified as unknown uses [p.17]). Moreover, the level of resolution of the GIS data set and protocols for reach classification employing such data are not specified. This further constrains any critical review of the proposed approach. The notion of a landscape multimetric index (p.17) also does not appear consistent with the ascription of levels of potential impact to classes of land use types adjacent to individual reaches. Explanation of the ordination and vector plot using PATN (Figure 6) is unconvincing. While, procedurally, performance may only need to be monitored when compliance is confirmed, it would be a sorry omission not to gauge performance at different levels of non-compliance (p. 6).

Appropriate maps and figures are to be incorporated. Problems regarding confounding gradients will be addressed during data collection and analysis. Will need to reassess site location and undertake further sampling if confounding effects are identified as a problem. 7 Problems with the site selection process are being addressed by re-writing the section to address many of the misunderstandings and uncertainties identified. Includes supplementation of gauging station sites at other reaches, with flow characteristics determined post hoc. This is acknowledged as far from ideal. It will need to be acknowledged as a weakness when analyses are undertaken. Determining if confounding gradients exist will be the subject of initial investigations. 8 Regarding analyses on flow gradients, it is stated that each indicator will form a separate flow regime gradient for analysis, and that this will be clarified. As part of the clarification, the likely number of sites per resultant gradient should be indicated, along with some consideration of the sensitivity of the power of the analysis to site number, etc.
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Given that only six variables were used (p. 18), it would have been useful to plot a series of graphs to allow assessment of each of their patterns. Better consideration of the meaning of summed variables (which can be an error-fraught process) is required. It is difficult to assess the validity of the site selection process given the paucity of information presented to the reader and the lack of clarity in that presented (e.g., table numbering is out of sequence for the entire document). Specific points of concern with regard to the derivation of a flow disturbance gradient are: Although it is stated that flow data are available for 33 stations, it is not stated how these data are analysed or positioned along some gradient of disturbance. How were/are deviations away from natural for each flow parameter assessed? Was it similar to the benchmarking process used in other WRPs? Is each flow indicator assumed to be as important as another? For example, is a 15% deviation in the floodplain zone statistic equivalent to a 15% change in median annual flow? Are they expected to result in equivalent change for each biotic component? Is a multivariate approach used to allocate sites to a disturbance gradient? If so, how was it done? It is stated (p 17) that sites were selected from river sections with IQQM data, yet in the preceding sentences it is stated that IQQM data and gauged flows will be used. Have sites been selected or not? If sites have indeed been selected, why is a map not presented so that the potential confounding influences or natural gradients can be assessed? If sites have already been selected, some indication of the spread of sites across the flow gradient is required (i.e., a histogram). Are sites equally distributed across the three categories (highly modified, moderately modified and unmodified) depicted in Figure 4? In summary, the most important design criterion, flow regime change, is inadequately described. Land use impacts are better described, yet there are some concerns here also. Reliance on unlisted Calvert et al. (2000) noted above. Without this reference objective assessment of the methods strengths or weakness is impossible. Nevertheless, the process describing how a land use disturbance gradient is better explained than it was for flow disturbance. The disturbance gradient needs to be expressed in one dimension only (acknowledged on p. 18). How is a single index to be derived from the multivariate approach? Why is this process not described? Why is there no indication of the distribution of sites along this gradient. Similarly, why is there no real indication of the spread of sites of known disturbance throughout the catchment (i.e. a map)? Why is the final landuse multimetric score combined with a score for adjacent landuse type? Is the latter accommodated by the reach scale measures? What is the outcome in the event that ground truthing reveals substantial incongruity between ratings based on maps and local inspections? It is important that the simultaneous distribution of potential study sites along both gradients be assessed (i.e. a three-dimensional histogram). Are they equally spread along both gradients? If not, this will have substantial implications for analysis. 9

Statistical methods. A nested gradient approach is appropriate for the kinds of investigations proposed here. However, some of the methods proposed above may prove difficult to accommodate within the design proposed. Throughout the document, there is a lack of information, or clarity in that information, as to what the predictions/hypotheses are and just what summary variables for each indicator are to be analysed.
9

It is stated that catchment boundary determination clarified the issue of what land is drained by particular reaches. Rewriting will clarify some misconceptions about scale of GIS coverage, field observations, etc. Other site-related issues are stated to have been addressed.
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Much is made of statistics and power analysis, but there is little mention of the type of data to be analysed. Invertebrate community structure is a nebulous term for which there are various types of measure which will be used? Richness? Multivariate scores? What variables associated with the fish investigations are to be analysed: richness, relative abundances of specific fish, total biomass? Similarly, what variables are expected to arise from laparoscopic inspections? The document would have benefited greatly from the inclusion of a table, or amendment to Table 3, listing output parameters from each of the investigations, and expected types of change for each variable (i.e., some hypothesis concerning the relationship with the flow regime). It is imperative to know what statistical methodology is to be used prior to data collection; otherwise it may be found that the design is inappropriate. At present, the document almost suggests that CSIRO and CRC CZ are to be called in at the end to analyse a large mass of data. The analytical procedure apparently relies greatly on regression procedures. At present there is no mention of precisely how the analyses are to accommodate one gradient nested within another (particularly when both are numerical rather than categorical). Is partial correlation analysis to be used? Multiple regression? Has any thought been given to blocking sites along each gradient (such as indicated in Figure 4), so that ANOVA procedures (ANCOVA, nested ANOVA, nested MANOVA) can be used to examine relationships between indicators and flow regime changes? Would an ANOVA approach be more powerful than regression approaches, particularly when the form of relationships between indicators and disturbance gradients are unknown? This requires consideration. 10 It is evident that four sampling trips are planned. How is the influence of different sampling occasions to be accommodated within a regression type approach? It is not clear how (c), p 21, will allow the identification of confounding natural gradients. Ecological Goals and Hypotheses (Table 3 etc.) The tabular presentation of indicators and methods is a good idea, but is currently inadequate. Examples of why this assessment has been reached are listed below. Each goal, hypothesis and indicator requires reworking to address the sort of issues raised. It would be expected that Table 3 would detail the measures associated with the indicators e.g. fish community structure might be described in a number of ways how will it be used here? How are fish larvae an indicator? Without such indication it is not possible to assess the validity of the methods. The impression at this stage is of a shot-gun approach that has not been adequately thought through. This may be untrue, but it is what the written evidence suggests. 1. Water quality. A proper discussion of water quality issues is required, providing the basis for a fully explicit water quality sampling design. For example, release of water may artificially improve water quality where it would otherwise have deteriorated naturally. Diel (or dawn/dusk) sampling is critical for DO and pH assessments, which may be greatly affected by flow regime. They are also greatly affected by the biomass of macrophytes (as are nutrients). DO, pH and nutrient measures may be next to useless without estimates of plant biomass (which do not appear to have been included in the program). How will flow affect turnover? How will this be monitored? The proposed sampling frequency will not help sort this out.

In response to queries about the statistical design and procedures, it is indicated that a CSIRO statistician has vetted them. Use of regression models is warranted by the continuous nature of the variables. Concerns about use of data from separate sampling occasions will be clarified. Note that two years data may show consistency over two years, but may not represent long-term consistency. Other concerns were probably the result of misunderstandings of how procedures were to be used.
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2. FPWF will stimulate recruitment, dispersal and spawning activity. The hypothesis that the first post-winter flood (FPWF) will achieve all these important functions with respect to fish assemblages relies largely on anecdotal data in Merrick and Schmida (1984), selective quotation of material in Pusey et al. (1999) (for example, the inference that increased spawning in Mogurnda adspersa occurs when water temperatures are elevated (Table 4) ignores the suggestion in Pusey et al. (1999) that northern populations of this species spawn in spring) and appears to be uncritically derived from the Arthington et al. (1992) explanation of the holistic approach. It must be noted that many fishes spawn during periods of low flow during the spring months. The FPWF may be detrimental to recruitment in these species if it occurs in October or November (i.e. it may be a source of mortality). Similarly, for those species that spawn during summer, is flood occurring in April likely to affect reproductive success as one occurring in February? Given that the pilot study is expected to last for two years only, these concerns are unlikely to be addressed properly. 11 The likelihood that the FPWF will maintain reproductive processes and movement of native flora & fauna (p. 24) in the riparian system is arguable. In light of (i) the general lack of knowledge of plant phenologies and precise triggers to phenological events, (ii) the great structural and floristic variation in these communities, and (iii) different species being differently stimulated, it is unlikely that there would be any candidate indicator. 12 3. Flows will maintain river character and behaviour. Whilst the hypothesis is reasonable, it is questionable whether the study can fully address this issue in its short time frame. It is not stated in the design particulars the length of time that reaches have been subjected to flow modification. Geomorphological responses to altered flow patterns typically take many years to become evident and any design proposing to define the extent to which flow manipulation impacts on channel structure must be mindful of the long time scales involved. Mapping would have to include variables such as soil type, which may confound other measures. 13 4. Maintain waterhole habitats. Certainly, this is a reasonable goal. Water holes can be vulnerable to altered flows (whether reduced or supplemented). We need to understand their seasonal dynamics degree of flushing, stratification, water quality diel cycling and seasonal changes, etc. Macrophytes may be an important component of the biota (and a major influence on water quality) and should be included in all assessments. 14 5. Riffle habitats etc. Maintaining riffle habitats may be a sensible goal if such habitats are permanent, but not if they would naturally dry (thus stimulating macrophyte reproduction, etc.), as often happens in such systems (this consideration may be incorporated within the natural variability). Again, understanding their natural dynamics is important for goal setting under altered flows.
Regarding FPWF, the proponents propose testing the most likely candidates; if none are established then mechanisms should be in place to address this issue and recommendations to this effect would be made as an output from this project. Were unclear as to what those recommendations might be perhaps they should be elucidated here. 12 Later they state that issues with the hypotheses for First Post Winter Flow are beyond the scope of this study. The flow indicators and hypotheses were not developed as part of this project. This response is inconsistent with the previous one, and essentially begs the question there is a point to be addressed here. Although the authors cannot be expected to achieve everything in two years, more explicit inclusions and exclusions are required in the proposal; and deficiencies in the brief need to be elucidated, if only to pave the way for an incomplete outcome. 13 The proponents acknowledge deficiencies in the geomorphology indicators and methodology; this problem will be addressed by a review conducted by Australian Geographical Science Organisation. How will the results of this review be incorporated? What is the timeline? 14 With regard to macrophytes, the proponent will add methodology, but doubt utility in relation to flow variables (to be confirmed in this study). Note that macrophyte assessment is a necessary adjunct to interpret water quality, given that plants are responsible for much of the water quality variability.
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6. Maintain riparian habitats. It is clear that flows in natural waterways are associated with responses in both the in-stream and nearstream communities. To date, attention has been focussed on detecting the relationships between flow regulation and in-stream assemblages particularly of freshwater fishes (Bowen et al. 1998, Hughes et al. 1998) and aquatic macroinvertebrates (Fore et al. 1996, Smith et al. 1999). Investigation of the impacts of flow regulation on other in-stream communities such as the aquatic macrophytes (e.g., Small et al. 1996) also appears to be in its early stages, and, apart from the work of Mackay and Thompson (1999), largely confined to those of northern hemisphere temperate streams, particularly in France (e.g., Bornette and Amoros 1991, 1996; Bornette et al. 1998). Impacts on the near-stream vegetation communities, however, seem to have received less attention and predictions are more reliant on generalisation and supposition. Despite this, work has been conducted in an attempt to elucidate the connection of riparian vegetation to stream flows. Nilsson et al. (1997:798) have documented the long-term responses of river margin vegetation in central Sweden to water level regulation and confirm that riparian ecosystems provide clear indications of environmental change. Because of its close dependence on streamflow, riparian vegetation can be very sensitive to changes associated with water development (Auble et al. 1999) and, therefore, provide reliable indicators of impact. In Australia, there is ample evidence for the decline of riverine and riparian vegetation along the River Murray being related to flow regulation (Walker 1993:33), and there is evidence of dieback due to irrigation-induced waterlogging in the Burdekin floodplain . Walker and Thoms (1993) document such a decline in the Murray as beginning in the 1930s but expanding greatly in the 1950s and provide some understanding of this impact. Explicit consideration of the coupling of components of annual stream flow hydrographs and the germination of certain riparian species can be found in Shafroth et al. (1998). This work, conducted along streams in Arizona, identified key hydrograph components including (i) timing and magnitude of flood peaks, (ii) rate of recession of the falling limb of the hydrograph, and (iii) the magnitude of base flows, that greatly influence seedling germination and, eventually, successful establishment. These results, based on four riparian species (3 native and 1 exotic), were considered to be generally applicable to other woody species in the riparian zone. Thus, despite obvious problems due to the complexity of near-stream systems and the lack of a large literature on links with stream flows, there have been some investigations. However, there is little within the draft document to suggest that there is an appropriate awareness understanding of that literature and how research findings might be incorporated into monitoring programs. Note that riparian indicators will be substantially affected by land use and degree of disturbance due to stock, weeds, fire etc. How will these variables be incorporated? 15 7. High flows will provide natural connectivity between watercourses and associated floodplain and wetland habitats to support natural flora and fauna. It is not immediately clear what is meant by natural connectivity in this hypothesis, or what indices are logically indicative of this important ecological process. Presumably, it refers to maintaining natural levels of inundation, frequency of inundation each year, length of inundation per spell, timing of inundation spell and not just the extent of inundation (i.e., wetted area). It is not clear whether all of these parameters can be estimated from satellite imagery (are images taken frequently enough, for example?). It may be appropriate to use standard hydrological and geomorphological techniques to model floodplain inundation extent and estimate spell lengths and frequencies by relating discharge, stage height and channel geometry and truthing these predictions against satellite imagery. It may prove difficult to accommodate this hypothesis within the nested gradient approach given that not all sites are likely to have associated floodplains or wetlands. The time frame necessary to understand the dynamics of these systems may reduce utility of the indicators. Indicators should include macrophytes
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as a key to water quality processes, habitat and ecological processes. What is meant by bird community structure simply the species list? Or is it abundance of species, or r interrelationships in the food web (which incorporates more of the notion of structure than richness and abundance)?. The obvious birds can have limited value as indicators as they can be transient; this is especially true for data collected using a limited sampling frequency. With regard to riparian communities, appropriate indices might be obtained from various existing studies that are not cited. Many focus on the extent and longevity of water level changes. The early work of Franz and Bazzaz (1977) that related the occurrence of riparian trees to inundation duration and that of Harris et al. (1985) that employed hydraulic simulation models to describe plant distributions along transects orthogonal to the stream channel would have provided useful models. These studies provide the foundation for the approach which links the present distribution of different cover types of riparian vegetation to inundation duration as derived from flow-duration curves. Instream dams or diversions have predictable influences on the flow duration curve and can be used in combination with gradient analysis to predict impacts. Inundation duration integrates or is correlated with flow-related variation in a range of variables such as shear stress, sediment deposition and erosion, depth to groundwater and to soil oxygen concentrations experienced in the riparian zone such that it has considerable potential as a predictor of vegetational change. Other multivariate measures associated with the impact of water level fluctuation might have been obtained from the more recent Australian work of Brownlow et al. (1994). 8. Mean wet season flow volume will maintain a) estuarine productivity, and b) estuarine habitats. Much of the eastern Australian data concerning fisheries catches and wet season flows do show a positive relationship between the two. However, the hypothesis as stated infers that this relationship is solely due to an effect on productivity (i.e. greater fisheries catches = greater productivity). This may not always be so as, in some cases, greater catches result from increased mobility and hence catchability associated with high flows. In some instances the opposite occurs. The hypothesis that estuarine habitats are dependent only on wet season flows ignores the other half of the year. The water quality measures need elucidating water quality cannot be applied as a simple catch-all. Each variable is complex, and can be even more so in estuaries, where tides, salinity, wind, etc. may have major influence. 9. Maintain Rare and/or Threatened species. At the outset, ensure that the proposed monitoring does not adversely affect these species! While it may be difficult to ascribe changes in Rare and Threatened populations to flow (or anything else), especially if population densities are very low, it is worthwhile monitoring the populations in any case. The exclusive focus on Rheodytes leukops (note that the species name is inaccurate in the draft text) is insufficient. While this endemic turtle is of very high conservation significance, the program should include other near- or in-stream plants and animal species. Elements of the flow regime other than base flow (e.g. first flushing flows and high flows) may have implications for rare and/or threatened species at particular stages of their life cycle (especially reproduction).

Selection of indicators, methods of data collection, time frames. Indicator selection.

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It is clear that a great range of candidate indicators and metrics have been investigated as surrogates for water quality, but the absence of specifics and simple reference to the TAP and Storey & Smith, 2001 (which does not appear in the bibliography and is useless to this review) is inadequate. 16 17 18 Timing and frequency of sampling. This is always a compromise between the desirable and the affordable. Biannual sampling will be adequate for the purpose for some measures, but not for others, where understanding of daily and/or seasonal dynamics is required (as indicated above). In some cases, event-based monitoring is important, while for others, avoiding events (especially floods) is important. Events may be postflood or minimum flow periods. Knowledge of antecedent conditions is critical, and appraisal of this should be explicitly included. Fully critical appraisal of timing against each measure is required. 19 Benthic metabolism. The incorporation of studies on benthic metabolism in an investigation of the effects of flow modification is laudable as even small changes in carbon production may translate into substantial effects in other parts of the food web. However, the process by which benthic metabolism will be incorporated into the design is not made clear. For example: nowhere is it stated how many replicate chambers are to be installed at each site on each occasion; it is not stated whether domes are to be positioned across all different habitat types or will sampling be stratified? how are changes in GPP and R24 values expected to change with differing levels of flow regime impact? as the domes are bottomless, some indication of their sensitivity to exchange in the substratum, and effects of different substrata, is required; there is no indication of what hypotheses are to be tested concerning flow manipulation and benthic metabolism; how will the impacts of antecedent flows be accommodated within the study design given the small number of sampling occasions? For example, elevated flows occurring a short time prior to sampling may have disturbed existing micro-algae or redistributed detritus. How are such effects to be considered? the construction and deployment of the domes is no easy task will it be done in-house or contracted out? The budget is insufficient for the latter. Does sufficient expertise exist within the team? Insufficient information is given to allow assessment of this component (the reference to Bunn et al. is inadequate). These concerns relate to the extent to which benthic metabolism can be related to discharge manipulation. Consider the example where flow manipulation results in an increase in available habitat across which some habitat patches, although limited in extent, become greatly autotrophic, whereas other patches remain heterotrophic. How is it intended to accommodate such effects? 20

It is acknowledged that the links between indicators and hypotheses need clarifying, and it is indicated that Table 3 will be amended accordingly(provide a short review of relevant literature for all indicators). 17 It is stated that the selection of indicators was primarily guided by the TAP report, as was necessary. This will be clarified. Nevertheless, alternative indicators should be discussed and considered for adoption, should they appear superior. 18 The authors state that water quality related to operation of infrastructure will be a compliance monitoring issue and was beyond the scope of this study, and that spot water quality measures will be taken at the time of sampling merely as a means of aiding in the interpretation of results. We stress the need to consider water quality as a flow-related issue; and we stress that spot measurements of water quality can be useless in any interpretation of conditions, given the dynamics of so many water quality measures. 19 Concerns about the timing and frequency of sampling are (and were) acknowledged. Again, any weakness due to the design must be properly included in any assessment. Previous comments about sensitivity apply here too. 20 Need for support for benthic metabolism methodology acknowledged, and to be added to the text. Expertise concerns to be addressed during the QA/QC process. Is this before or after samples have been collected?
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Macroinvertebrate community structure. While the AusRivAS methodology may be appropriate, a proper description of how it will be applied, and a critical appraisal of it (e.g. arguments about effects of inclusion or exclusion of rare taxa) are required. It is assumed that by structure, it is composition (including relative abundance) that is actually meant, as structure implies functional links that are not a component of the study. Studies of fish in the Fitzroy are reviewed, but not of the invertebrates why? An explanation of the sample design and techniques is required. For example, at what depths will water holes be sampled? What sampling devices will be used? Will macrophytes be included? How will different substrata be incorporated? Are riffles permanent (it is not clear from the report)? For the wetlands, we need to have more information on how macrophytes might be included. How will samples be quantified? How many replicates per habitat, per substratum, per macrophyte species are to be sampled? 21 Fish cohorts, community structure and fish movement. Table 4 does not appear to be referred to in the text, and is, in any case, out of place in this document. The sampling methodology proposed to collect fishes is, in general, adequate providing that the following concerns are addressed: The sampling protocol developed by Pusey et al. (1998) is intended for use in streams and rivers with depths less than about 1 m. It is inappropriate to employ this method elsewhere, such as in water holes. The extent to which the QDPI sampling methods address this problem is unknown as no details or references are supplied. Water holes are apparently of great significance in the Fitzroy River, yet no method for sampling fishes in these habitats is described. The sampling protocol of Pusey et al. (1998) is intended to supply quantitative data on fish density and biomass. Other methods currently employed in Queensland provide data only in terms of catch per unit effort. What are the expected units in the proposed study? What are the indicator metrics species richness, biomass, density? It is stated (p. 30) that individual hydraulic units in each site will be sampled and then data pooled. This approach is analytically appropriate only when all sites contain the same array of hydraulic unit habitat types. The analysis would be much more powerful if it were stratified to accommodate between-site differences in habitat availability and extent. The same concern applies to the use of supplementary seine netting. There is comment (p. 37) on the need for rare and threatened species requiring particular attention. However, nowhere in the document is any mention made of fish species of high conservation status. The Fitzroy River contains one endemic species (Saratoga), one endemic subspecies (Yellowbelly) and another species of limited distribution (Leathery grunter). The first two species are of recreational fishing significance. Surprisingly, no mention is made of these species (other than in Table 4). Yellowbelly and Leathery grunter both make flowrelated spawning migrations and are thus likely to be affected by flow regulation. Saratoga spawn during spring and are thus likely to be negatively affected by an early FPWF. No measures are suggested that would allow an examination of the impacts of flow regulation on these species. Note that larval sampling is unlikely to collect any of these species because (i) Saratoga are mouth brooders, and (ii) potadromous spawners that make large migrations and produce pelagic eggs do not produce many pelagic larva that can be sampled for example, Humphries and colleagues have failed over many years to collect a single Yellowbelly larva by conventional passive sampling means. The proposed design includes provision for larval fish sampling but the authors also state that larval fish sampling will not be continued in the final monitoring program, rather some supposed relationships between juvenile cohort size and age/length relationships yet to be developed by a student under a yet to be confirmed supervisor will be used to examine the impact of flow regulation. The authors correctly note that flow regulation might depress
The proponents state that concerns about the macroinvertebrate sampling might be addressed by adding the indices that will be calculated from the data and that the comments were unclear and so difficult to address. The questions in this paragraph are very clear, and have not been addressed for example, the number of replicates per habitat is easy to answer (and has a direct bearing on the quality of the data and the cost of the exercise).
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recruitment by removing conditions necessary to stimulate spawning, or failing to sustain those larvae produced. The proposed juvenile recruitment method will not allow an objective assessment of the extent to which either of these two factors contribute to any recruitment failure that may develop. [NB see note below about student projects and appropriate supervision.] It is stated that larval fish abundance will not be used to examine flow/recruitment relationships. Rather, presence/absence will be the indicator of choice. Many species of fish produce small numbers of larvae year-round although most larval production occurs during better defined periods, which may or may not be related to flow regime (see Pusey et al. 2001). A presence/absence approach will not be useful with respect to these species, which probably make up the bulk of fishes present. Therefore, this approach will be unlikely to provide any meaningful assessment of the impacts of flow regulation. Cohort analysis relies on the presence of distinguishable cohorts. This is often very difficult in Queensland fish populations due to prolonged breeding seasons and variability of flow. How will this be accommodated in the design? It is stated that some larval fishes are difficult to identify. How will this problem be overcome? None of the hypotheses concerning flow/fish were generated using data from the Fitzroy River (noting that this river is apparently one of the most variable in the world). Are the hypotheses, therefore, appropriate? Fish movement is not addressed anywhere yet is a critical component of any program addressing the effects of flow regulation on fishes. What would be the purpose of estimating fish weight from length measurements if one is directly correlated with the other? Would real weights be useful to show deviation from the relationship, indicating condition? The student project supervisor should be someone with knowledge of Australian fresh waters and freshwater fish. It is also questionable whether it is appropriate to rely wholly on a student project (although great value could be added by having non-essential projects attached to the study). 22

Turtles. Turtles are a significant vertebrate component of any Queensland river and the inclusion of this taxon is appropriate. However, whilst acknowledging the high conservation status of R. leukops, the program should be expanded to include other species, particularly as they will be collected at the same time as R. leukops (p. 38). It is assumed that discussions have been held with appropriate turtle researchers such as Col Lympus and the proposed collecting regime may be the most effective, although dismissal of funnel trapping maybe too hasty would it not be worth trialling the method? But, while monitoring turtles is appropriate, are they likely to be useful as indicators? Are the investigators able to distinguish different turtles species at night under spotlighting conditions? The principal concern with the method is that it may prove difficult to incorporate the collecting data into a valid statistical analysis. Other concerns include: It is not clear why turtles are tagged upon capture. Are the investigators intending to estimate population sizes (by mark recapture techniques), estimate growth, estimate habitat use or

The proponents state that (i) the brief for the PhD project on fish larvae will clarify some of reviewers questions; (ii) the sampling protocol for deeper sections of the river has been determined in consultation with DPI fisheries (using a boat-mounted electrofisher); (iii) they will sample appropriate areas with a backpack electrofisher; (iv) hydraulic units within sites will be analysed separately; (v) derived indices from the raw fish data will be included; and (vi) while the question regarding fish movement is valid, the resources of the project are insufficient to address it; it is a major contender for further investigation. The reviewers acknowledge that at least some of their concerns are being addressed, but cannot comment further without seeing the items in question. Judgement about available resources is surprising given other proponents comments regarding ignorance of the budget.
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movement patterns? Some discussion of the methods proposed if any or all are intended would be useful. It is unclear how laparoscopic investigation can provide the data stated, but more importantly, it is unclear which personnel are to perform this examination. Presumably substantial expertise is required to ascertain breeding status does this expertise already reside in the project team? From the budget/costing details presented on pages 44 & 45 (i.e. $99.25/site), it is assumed that outside consultants will not be used. However, the stated method suggests at least 4 person/hours of snorkelling, plus some undefined period of spotlighting, plus laparoscopic investigation, plus location, inspection and measurement of nesting sites will be required. How can this be achieved for only $99 per site? How is it intended that data on nest location, fox activity, breeding biology be analysed? 23, 24

Physical and chemical characteristics of in-stream habitats. There appear to be some misconceptions about habitat structure and its measurement. For example, the Instream Flow Incremental Methodology approach does not assess the condition of water resources (it models habitat responses to varying discharge) (p 38), and quantification of the amount of habitat does not necessarily allow a surrogate measure of the potential abundances of biological communities. This point assumes that habitat availability is the limiting resource. The authors correctly identify that aquatic habitat needs to be considered at a variety of scales, yet the proposed sampling regime does not facilitate such an examination. The SoR approach was designed to allow an assessment of river condition; it was not designed for complex habitat mapping nor does it yield data amenable to statistical examination in the design proposed here. Information of habitat structure (flow, depth, substrate composition, the presence of woody debris, etc.) needs to be collected within a random points design involving substantial replication. Other important points: The intention of the cross-sectional surveying is not immediately clear. It appears that it is required to explore indicator criteria for both river geomorphology and waterhole structure. Given the difference in scales, both spatial and temporal, can the same method be used for both? It is not clear how cross-sections will be related to flows given the possible confounding criteria such as soil type, gradient, vegetation, etc. Explain how transect positions will be located on subsequent sampling occasions. Will the limited temporal examination allow seasonal differences in habitat structure to be fully appreciated? How are antecedent flow events accommodated? Why are velocity and depth the only variables to be measured along each transect? Why not substrate composition, presence of macrophytes, woody debris? All are expected to varying according to flow regime. Throughout the document, emphasis is placed on two important habitat types, namely riffles and water holes (pools). It is possible that a single surveying/mapping methodology may not be achievable. Two water quality variables (temperature and DO) are to be measured. Presumably these variables are important as indicators for deteriorating water quality in water holes. However, this seems to be a very sparse assessment of water quality (see below). It is therefore assumed that other water quality variables will be measured. However, no details about which parameters are to be measured are given. Are nutrients to be measured? Pesticides? What variables will allow land use effects to be factored out in the final analyses?
The proponents state that concerns about the turtle methodology will be addressed; it is being developed in conjunction with A. Georges of University of Canberra (expert on turtles). 24 The authors state concern about the exclusive focus on Rheodytes leukops as the rare and threatened species to be monitored is beyond the scope of this study. This was the only R&T species identified in the TAP report of the WRP as being potentially influenced by water management. Nevertheless, comment is expected; and if the TAP has erred, it should beholden upon a consultant to point it out.
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How will DO, pH be related to macrophytes (which do not appear to have been included)? A water quality sampling design is required, addressing the above points and other issues such as diel (or dawn/dusk) sampling critical for DO and pH, both of which may be greatly affected by flow regime. Is turbidity to be measured? This will be of great relevance to benthic metabolism, and may be important in determining the distribution of R. leukops (Cann, 1998:239). Note other problems with water quality assessment, discussed above.

It must be stressed that habitat structure (including aquatic plants) may have substantial consequences in determining the presence/absence of particular species, their abundance (under special circumstances), condition and reproductive success. It is therefore critical that habitat structure (including dispersal barriers) be quantified so that it may be meaningfully incorporated in the statistical analysis. Note that costings for geomorphological examinations are not included in Table 6 (although they are for Table 5). Riparian habitat, vegetation community structure and canopy cover. How useful is riparian vegetation as an indicator in the short term, given that responses to changed flow regimes may take years to be measurable? It is apparent here that there is some understanding of the functional importance of the near-stream communities and of the utility of incorporating these components into metrics used to assess stream health. Recognition that the often poor condition of the riparian verge is due to non-water resource related factors (especially clearing, uncontrolled stock access and exotic species invasions) is clearly warranted at the outset, as these factors greatly confound the exercise of teasing out impacts on the riparian zone that are expressly flow-related. The SoR approach to be adopted, while generally appropriate for an assessment of gross condition, appears largely inadequate within a nested gradient approach to the determination and monitoring of flow-related impacts on this component. While the author of the SoR assessment method to be adopted himself claims that the derivation of a single variable or index of riparian condition is an impossible task (Anderson 1993:15), the use of a rating system to combine several attributes is most reliant upon observer standardisation and relies also upon botanical knowledge on the part of an observer or monitoring team to identify major species and to discriminate between native and exotic species. These can be inadequacies already detectable in SoR data sets and it is an issue that is distinctly relevant to data interpretability and should have been addressed as part of a detailed proposed methodology. While single scores (usually ranked or ordinal), however derived, can tell us a great deal, they are difficult to interpret in isolation and without the application of considerable expertise. There is a need to clarify the notion of a vegetation scaling factor that relates to vegetation density (p. 39). Anderson (1993:97) does state that his method of riparian vegetation condition assessment employs a combination of the reduced cover compared with a regional or catchment standard, but due to the degree of modification of the riparian zone previously alluded to, such standards may well be elusive. This is an issue that deserves some consideration. There are some misconceptions evident in the wording of the draft text. Presumably FPC refers to projective foliage cover (more properly PFC) as a conventional attribute in Australian vegetation structural classificatory systems rather than foliage protection cover. Such simple errors of translation of existing vegetation science protocols do not instil confidence in the study. The assessment of a 100-metre section of both banks rather than a narrower (or undefined) swathe at 25 metre intervals is preferable to a single transect at a given site; however, our experience suggests that the inherent variability within riparian communities will not be comprehensively captured. Firsthand experience in the Pioneer and Proserpine River systems indicates that a significant time allocation at each reach is required to undertake such survey accurately and comprehensively. In
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addition, there is still no way the representativeness of the sample can be adequately determined without much greater effort to ascertain this from more synoptic aerial photographic coverage or by some other means. Aspect, in many instances, is a major determinant of riparian zone structure and floristic make-up. This has not been adequately addressed in any of the dedicated methodologies yet derived. Moreover, no detail is provided as to how evidence of regrowth, dieback and other indications of disturbance (p. 40) will be recorded. There are, of course, some standard forestry mensuration techniques available to which reference might have been made. 25 Frogs. The proposed focus on frogs as an indicator group is laudable but fraught with problems. While often sensitive to environmental changes because of their permeable skin that makes them closely linked with the ambient environment, frogs are also a diverse group of organisms. Some are highly reliant upon access to wetland breeding sites while others are obligate lotic stream dwellers, and others still do not possess a free-living tadpole stage and instead are reliant upon access to a moist leaf litter substrate. It is not clear how the sampling design for frog data collection might be related to flow regime. The authors recognise that frogs are difficult to incorporate in monitoring programs (p. 41) and they suggest that automated recorders are the most appropriate way of broad-scale sampling. Such a sampling technique, if employed at regular intervals at appropriate sites (e.g. a reliable wetland where frogs congregate to breed) and the most appropriate time during the year (and this may well not coincide with the two proposed sample periods) can provide local or district trends in frog assemblage composition and relative species abundances. These trends, however, are unlikely to be directly related to flow changes in a river system but to broader climatic oscillations and/or land uses surrounding a strategic wetland, and certainly could not be confidently interpreted as reliably representative of this group. Automated recording of singing males can only be used to determine species richness of frogs at a particular site and is not wholly appropriate for measuring abundance, unless sampling intervals approximate the repetition rate of individual species (Heyer et al. 1993) or call intensity is somehow averaged over time, and overall intensity is used as a surrogate for abundance. It is not recommended for comparing different sites or for species with explosive breeding cycles. Given these constraints, it may prove difficult to monitor frogs. However, in view of the substantial difficulties in incorporating frogs into rapid assessment protocols using other methods, it is considered worthwhile to trial this methodology. 26 Bird community structure. The inclusion of birds in the program is valid as many species can be reliant upon the integrity of riparian zones and can be a useful indicator group. However, different species exhibit very different associations with water bodies: some are sedentary residents, others seasonal (including international) migrants, while others (e.g., honeyeaters) are very irruptive or nomadic. Additionally, impacts on the riparian zone may not show up for several years. It will therefore be difficult to demonstrate any effect of flow regulation on bird communities. However, it would be useful to develop a standard system through which a subset of the bird community might be reliably linked to flow regime change,

The proponents state that riparian data is collected by a modified SoR method by experienced DNR&M staff. Where necessary, specimens are collected for later identification. Both raw data and the derived condition rating will be used. The FPC/PFC error will be corrected. 26 With regard to climate variations, the proponents see frogs as little different from other indicators, in that all have difficulties associated with them; however, the projects gradient approach should factor out these type of large scale overarching sources of natural variation. This will depend on whether the gradients capture the change gradients. In any case, climatic variability is an inherent consideration in any field-based ecological study, and may have a unpredictable effects on environmental attributes (indicators), especially over a short study period. Not much can be done about this in the length of time available, apart from having adequate climatic records, a large number of sites, and gradients that include extremes.
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for this and other WRP areas. The collaborative venture with Griffith University will add value to the project, although it will be unlikely to contribute directly to it within its own time frame. 27 Estuarine indicators. The proposed estuarine methodology is weak. Is it possible to include other estuaries as benchmarks or as part of a gradient? The possibility needs discussion, even if it is not viable. The time required to be able to link any measures to flow variation is likely to be unacceptably long. Reference to outputs of the CRC project is not adequate the methodology should be described if it is to be adequately assessed. The same applies to assessment of mangroves and physical characteristics. How would other cumulative effects of long-term changes be factored out? Note that end of system indicators such as the size of the annual fisheries catches are usually associated with the volume of stream flow rather than the flow regime per se. 28, 29 Mangrove community structure. The investigation of trends in the relative cover of this community type from historical aerial photographic interpretation is a standard and reliable technique. The linkage between mangrove cover and flow regimes is less well understood. Given the opportunity to involve some specialist investigation of this component, its inclusion is a positive aspect of this draft proposed program. Physical characteristics and estuarine geomorphology. The above comments apply similarly here. Projected Costings It is difficult to comment on the budget without a detailed, itemised design to justify it (sites, replicates, etc). It is surprising that the birds cost more than the bugs, given the processing time for the invertebrates. 30 General observations/impressions The draft proposal clearly needs much work to produce an adequately detailed and justified monitoring program. In addition, there are some obvious misconceptions in relation to some biological components that warrant attention. There also appears to be a lack of review of the many techniques that are available or have been trialled and which might have been assessed with regard to their utility. There is a distinct lack of detail in those protocols proposed that constitutes a the major shortcoming. Questions as to how the investigation will be practically undertaken, and at what sites at what
The proponents state that the bird indicator will be fleshed out to include potential indices and a detailed project brief for the PhD project. Note that current projects include not only C. Cateralls group at Griffith University, but also bird and vegetation studies funded by the LWA Riparian Program at Charles Sturt University (contact Dr. Amy Jansen) and James Cook University (contact George Lukacs). 28 The proponents state that Details of the linked CRC Coastal Zone projects will be provided in separate appendices or the document will become too unwieldy. Nevertheless, this part of the proposal is not assessable because it is not presented how it fits the project, whether the methodology is appropriate for this project (as opposed to the CRCs brief), whether the CRC projects can deliver within the timeframe are all considerations that need to be assessed. We repeat that the estuarine section is particularly weak because of this deficiency. 29 The authors agree with the issues raised about estuarine productivity and using fisheries catch data as a measure of this. This, however, was the basis of the TAP findings about flows and estuarine productivity. We recommend that they take the opportunity to comment and put up appropriate alternatives. TAPs are not infallible (nor are consultants), and constructive criticism never goes amiss. 30 The authors respond to the comments about the budget by stating that budgeting is beyond the scope of the project as funding is determined separately. We do not understand this comment. As costing and design are inseparable, we would expect comment regarding limitations, number of samples, etc.
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locations and how will the various sites be accommodated across multiple environmental gradients continually arise. The possibility of confounding effects is recognised, but such effects are not properly detailed. There are, however, some positive signs within the document. The adoption of a nested gradient approach is a logical step to ascertaining flow-related impacts on an array of ecosystem components within a complex landscape context. This is so despite the scientific techniques being difficult to apply in the field and often awkward to interpret with regard to the major objective of such a research program. Opportunities to collaborate with specialists have also been taken and will add value to the research program. Unfortunately, the need for observer standardisation and some specialist biological knowledge is not identifiably addressed and may pose considerable difficulties for program implementation. Style etc. There are problems with use of tense throughout the document. It appears that this may have arisen from cutting and pasting from other documents without subsequent editorial checking. This may also explain the problems with reference citation. There are errors of nomenclature, in table referencing, and many omissions from the bibliography that severely constrain this review process. The writing is reasonably clear, at a technical level, but the informed layperson would find the going tough. Some rules are broken: e.g., never put a semi-colon after and it performs like a full stop; and dont use the semi-colon to introduce a list or an idea: the colon is the correct mark (as here). Use semi-colons to separate clauses of equal weight (as here); and use them to separate items in complicated lists (as has been done in some cases). One or two sentences lack verbs, theres mixing up of effect and affect, and other minor misdemeanours. While seemingly trivial, such deficiencies do detract from clear communication and lead to impressions of imprecision. They can be readily corrected by an experienced proof-reader.

References. Anderson, J. R. (1993) State of the Rivers Project: Report 1. Development and Validation of the Methodology. Consultants Report to Department of Primary Industries, Brisbane:127pp. Auble, G. T., Friedman, J. M. and Scott, M. L. (1994) Relating riparian vegetation to present and future stream flows. Ecological Applications 4(3):544-554. Auble, G. T., Friedman, J. M., Scott. M. L. and Shafroth, P. (1999) Gradient models predicting changes in riparian vegetation from altered stream flow. Current Research Project Synopsis - USGS Midcontinent Ecological Science Center, Fort Collins. http://www.mesc.nbs.gov/projects/gradient_models_streamflow.html Bornette, G. and Amoros, C. (1991) Aquatic vegetation and hydrology of a braided river floodplain. Journal of Vegetation Science 2:497-512. Bornette, G. and Amoros, C. (1996) Disturbance regimes and vegetation dynamics: role of floods in riverine wetlands. Journal of Vegetation Science 7:615-622. Bornette, G., Amoros, C. and Lamouroux, N. (1998) Aquatic plant diversity in riverine wetlands: the role of connectivity. Freshwater Biology 39:267-283.
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Bowen, Z. H., Freeman, M. C. and Bovee, K. D. (1998) Evaluation of generalized habitat criteria for assessing impacts of altered flow regimes on warmwater fishes. Transactions of the American Fisheries Society 127:455-468. Brownlow, M. D., Sparrow, A. D. and Ganf, G. G. (1994) Classification of water regimes in systems of fluctuating water level. Australian Journal of Marine and Freshwater Research 45:1375-1385. Cann, J. (1998) Australian Freshwater Turtles. Beaumont Publishing Pty Ltd, Singapore: 292pp. Cann, J. (1998) Australian Freshwater Turtles. Beaumont Publishing Pty Ltd, Singapore: 292pp.. Environment Australia (2002) Catchment, River and Estuary Condition in Australia: A Summary of the National Land and Water Resources Audits Australian Catchment, River and Estuary Audit 2002. Commonwealth of Australia, Canberra:19pp. Fore, L. S., Karr, J. R. and Wisseman, R. W. (1996) Assessing invertebrate responses to human activities: evaluating alternative approaches. Journal of the North American Benthological Society 15(2):212-231. Franz, E. H. and Bazzaz, F. A. (1977) Simulation of a vegetation response to modified hydrological regimes: a probabilistic model based on niche differentiation in a floodplain forest. Ecology 58:176183. Harris, R. R., Risser, R. J. and Fox, C. A. (1985) A method for evaluating streamflow discharge-plant species occurrence patterns on headwater streams. (in) Johnson, R. R., Ziebel, C. D., Patton, D. R., Ffolliott, P. F. and Hamre, R. H. (eds) Riparian Ecosystems and Their Management: Reconciling Conflicting Uses. United States Forest Service General Technical Report RM-120:87-90. Heyer, W.R, Donnelly, M.A., McDiarmid, R.W., Hayek, L.C. & Foster, M.S.. (1993) (eds.). Measuring and Monitoring Biological Diversity: Standard Methods for Amphibians Smithsonian Institute Press, Washington. http://www.mesc.nbs.gov/projects/gradient_models_streamflow.html Hughes, R. M., Kaufman, P. R., Herlihy, A. T., Kincaid, T. M., Reynolds, L. and Larsen, D. P. (1998) A process for developing and evaluating indices of fish assemblage integrity. Canadian Journal of Fisheries and Aquatic Sciences 55:1618-1631. Mackay, S. J. and Thompson, C. (1999) Flow requirements of submerged aquatic macrophytes. (in) Arthington, A. H. and Zalucki, J. M. (eds) (in prep.) Environmental Flow Requirements Downstream from Wyvenhoe Dam. SEQ Waterboard/CCISR, Griffith University, Brisbane: Chapter 7. Nilsson, C., Jansson, R. and Zinko, U. (1997) Long-term responses of river-margin vegetation to water-level regulation. Science 276(5313):798-801. Pusey B. et al. (2001) Proc Roy Soc 110: 26-47. Shafroth, P. B., Auble, G. T., Stromberg, J. C. and Patten, D. T. (1998) Establishment of woody riparian vegetation in relation to patterns of streamflow, Bill Williams River, Arizona. Wetlands 18(4):577-590. Small, A. M., Adey, W. H., Lutz, S. M., Reese, E. G. and Roberts, D. L. (1996) A Macrophyte-based rapid biosurvey of stream water quality: restoration at the watershed scale. Restoration Ecology 4(2):124-145. Smith, M. J., Kay, W. R., Edwards, D. H. D., Papas, P. J., Richardson, K. St J., Simpson, J. C., Pinder, A. M., Cale, D. J., Horwitz, P. H. J., Davis, J. A., Yung, F. H., Norris, R. H. and Halse, S. A. (1999) AusRivAS: using macroinvertebrates to assess ecological condition of rivers in Western Australia. Freshwater Biology 41:269-282.
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Walker, K. F. (1993) Issues in the riparian ecology of large rivers. (in) Bunn, S. E., Pusey, B. J. and Price, P. (eds) Ecology and Management of Riparian Zones in Australia. Occasional Paper No. 05/93, CCISR, Griffith University:31-40. Walker, K. F. and Thoms, M. C. (1993) Environmental effects of flow regulation on the River Murray, South Australia. Regulated Rivers: Research & Management 8:103-119.

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